#19,297
The two main H5N1 genotypes (out of > 100) we are watching in the United States are the B3.13 `Bovine' strain which emerged in Texas Cattle in early 2024, and the D1.1 avian strain that appeared in Canada the following fall and quickly spread through wild birds and poultry across the continent.
From a distance, it appears that the B3.13 strain produces mainly mild illness in humans (ie. conjunctivitis), while the D1.1 strain has been linked to a number of severe illnesses and several deaths.
But appearances, particularly when surveillance and testing are limited, can be deceiving.
- Bovine B3.13 H5N1 infections are probably easier to track because they occur on dairy farms, are more likely to be treated with antivirals, and may be more likely due to `splash' events where infection occurs through the ocular route.
- While many D1.1 infections occur on poultry farms, it may also be encountered by the general public through contact with wild birds and/or backyard poultry, which makes it more difficult to track.
In one study using human nasal and airway organoids, D1.1 appeared to be better adapted to human physiology, while in another (see IJID study) B3.13 caused severe disease, extra-respiratory spread, and lethality in ferrets while D1.1 caused milder disease with no lethality.
To be fair, differences in methods and materials used in these studies can make a huge difference in their outcomes.
- Some studies have used laboratory-propagated, clinical-origin H5N1 isolates, while others have used full-genome reverse-genetics reconstructions, or engineered PR8 reassortants carrying the relevant H5 and N1 genes from each genotype.
- Some studies used co-housed ferrets, or adjacently-housed ferrets (for airborne transmission), while others used organoids or other in vitro proxies to study replication or receptor binding.
All of which serves as prelude to a new preprint (not yet peer reviewed) which tested transmission and pathogenicity of D1.1 and B3.13 genotypes in co-housed ferrets.
Using primarily full-genome reverse-genetics viruses, these researchers found that - out of the box - the B3.13 genotype appeared to be better adapted to mammalian hosts than D1.1.
They cite:HPhTX B3.13 infection resulted in more severe clinical disease and enhanced viral shedding, with evidence of increased transmission relative to HPhLA D1.1.
But
. . . HPhLA D1.1 showed rapid acquisition of the mammalian-adaptive mutation E627K in infected ferrets and both E627K and Q194K in the only fatal contact animal.
The B3.13 used in this experiment was better adapted, but more stable. D1.1 appears to be more of a wildcard. While neither have acquired the ability to spread efficiently among humans, both require continued monitoring for further changes.
This is a lengthy (66 pages) and at times technical paper, so I've only posted the abstract and some excerpts from the conclusion. Those desiring a deeper dive will want to follow the link to read it in its entirety.
I'll have a bit more after the break.
Enhanced Pathogenicity and Contact Transmissibility of Human-origin Avian Influenza H5N1 Clade 2.3.4.4b Genotype B3.13 Compared to D1.1 in Ferrets
Ahmed M. Elsayed, Ramya S. Barre, Mahmoud Bayoumi, Alvaro Padron, Hossein Batebi, Vinay Shivanna, Roy N. Platt, Fiona Burmeister, Joshua Castro, Arash Rahmani, Juliane Lang, Chengjin Ye, Timothy J.C. Anderson, Roland Netz, Aitor Nogales, Robert P. de Vries, Geert-Jan Boons, Adolfo Garcia-Sastre, Elsayed M. Abdelwhab, Gregory C Ippolito, Luis Martinez-Sobrido
doi: https://doi.org/10.64898/2026.08.10.744032
This article is a preprint and has not been certified by peer review
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Abstract
Since its emergence in 2020, multiple genotypes of the H5N1 clade 2.3.4.4b have been identified, with B3.13 and D1.1 emerging in the USA as two major and concerning genotypes. However, their relative pathogenicity and transmissibility in mammals have not been fully elucidated.We compared the pathogenicity and transmissibility of the first two human H5N1 clade 2.3.4.4b cases caused by B3.13 in Texas (A/Texas/37/2024; HPhTX B3.13) and D1.1 in Louisiana (A/Louisiana/12/2024; HPhLA D1.1) in a ferret model of infection and transmission.HPhTX B3.13 infection resulted in more severe clinical disease and enhanced viral shedding, with evidence of increased transmission relative to HPhLA D1.1.Histopathological analysis revealed more extensive lung pathology in animals infected with HPhTX B3.13, consistent with increased viral loads and inflammatory responses. Importantly, both genotypes showed no significant differences in reactivity to ferret sera raised against candidate vaccine virus (CVV) strains, receptor binding properties, or neuraminidase (NA) activity and thermostability.Whole-genome sequencing revealed no adaptive mutations in HPhTX B3.13 following infection or transmission. In contrast, HPhLA D1.1 showed rapid acquisition of the mammalian-adaptive mutation E627K in infected ferrets and both E627K and Q194K in the only fatal contact animal.Both mutations were associated with enhanced polymerase activity and computational analyses suggested that they enhance interactions with the mammalian host factors ANP32A and B.Our findings indicate that B3.13 is already well adapted for mammalian infection and transmission whereas D1.1 retains evolutionary potential through the rapid acquisition of adaptive mutations, highlighting important genotype-specific differences relevant to zoonotic risk assessment and pandemic preparedness.
(SNIP)Overall, our study supports a model in which mammalian adaptation of contemporary HPAIV H5N1 is driven predominantly by optimization of viral polymerase function rather than by changes in receptor specificity. The genetic stability of HPhTX B3.13, together with its high polymerase activity, efficient transmission, and increased pathogenicity, suggest that this genotype is already well adapted for mammalian replication.
In contrast, HPhLA D1.1 remains incompletely adapted but rapidly acquires mammalian-adaptive PB2 mutations during replication in ferrets. The identification of PB2 Q194K as a cooperative mutation that enhances the activity of PB2 E627K expands our understanding of influenza polymerase adaptation and identifies a potential molecular marker for the surveillance of emerging H5N1 viruses with increased zoonotic potential.
Finally, this study has some limitations.
First, transmission was assessed in a single mammalian model with a relatively small sample size under controlled laboratory conditions, which may not fully recapitulate natural exposure settings or host diversity.
Second, only one isolate per genotype was evaluated. Third, the potential contribution of sex to pathogenicity or transmission was not assessed since only female ferrets were used in this study and because some previous studies used male ferrets 17,72 .
Finally, our in silico computational analysis suggested that the PB2 mutations 194K and 627K affect PB2-ANP32 binding in a host-dependent manner, with APN32A maintaining a more stable association than ANP32B and showing reduced binding stability. However, future studies are needed to confirm this hypothesis.
(Continue . . . )
The caveat to all of this is that while neither genotype appears ready for prime time - both were collected back in 2024 - and evolution never stops. Existing genotypes evolve slowly through antigenic drift or adaptation, while new genotypes can emerge via reassortment (antigenic shift).
We've even seen new subtypes emerge (see J. Virology: Risk assessment of avian influenza A(H5N5) virus from the first human case using the ferret model) during this epizootic.
There are no guarantees how long B3.13 - or D1.1 - will remain the primary HPAI threats going forward.
Right now, as the days grow shorter in the Northern Hemisphere, migratory birds that spent their summer in their high latitude roosting spots are starting to move south (see Sci Repts.: Southward Autumn Migration Of Waterfowl Facilitates Transmission Of HPAI H5N1).
While it is always possible the next wave will be less virulent, last year South Korea's MAFRA reported 3 different subtypes of HPAI (H5N1, H5N6, H5N9) in wild birds, and significantly increased infectivity.
Which makes now a good time for poultry producers - from commercial operations to back-yard hobby farms - to review their biosecurity procedures, and to make necessary adjustments before the fall wave arrives.
